A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions
文献类型：期刊论文
| 作者 | Yang, Zhuo2,3; Liu, Yingtao3; Chen, Zhaoqiang3; Xu, Zhijian3 ; Shi, Jiye1; Chen, Kaixian3; Zhu, Weiliang3
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| 刊名 | JOURNAL OF MOLECULAR MODELING
 |
| 出版日期 | 2015-06 |
| 卷号 | 21期号:6 |
| 关键词 | Halogen bonding sigma-hole Protein-ligand interaction Quantum mechanics Scoring function |
| ISSN号 | 1610-2940 |
| DOI | 10.1007/s00894-015-2681-6 |
| 文献子类 | Article |
| 英文摘要 | A quantum mechanics-based scoring function for halogen bonding interaction, namely XBScore(QM), is developed based on 18,135 sets of geometrical and energetical parameters optimized atM06-2X/aug-cc-pVDZ level. Applying the function on typical halogen bonding systems from Protein Data Bank demonstrates its strong ability of predicting halogen bonding as attractive interaction with strength up to -4 kcalmol(-1). With a diverse set of proteins complexed with halogenated ligands, a systematic evaluation demonstrates the integrative advantage of XBScore(QM) over 12 other scoring functions on halogen bonding in four aspects, viz. pseudo docking power, ranking power, scoring power, and genuine docking power. Thus, this study not only provides a practicable scoring function of halogen bonding for high throughput virtual screening, but also serves as a benchmark for evaluating the performance of current scoring functions on characterizing halogen bonding. |
| WOS关键词 | HIV-1 REVERSE-TRANSCRIPTASE ; RATIONAL DRUG DESIGN ; BINDING AFFINITIES ; FORCE-FIELD ; NONCOVALENT INTERACTIONS ; MOLECULAR-INTERACTIONS ; NONNUCLEOSIDE INHIBITORS ; DENSITY FUNCTIONALS ; GENETIC ALGORITHM ; ACCURATE DOCKING |
| 资助项目 | NNSF[81273435] ; NNSF[81302699] ; Ministry of Science and Technology[2012AA01A305] ; International Science and Technology Cooperation Program of China[2014DFA31130] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biophysics ; Chemistry ; Computer Science |
| 语种 | 英语 |
| WOS记录号 | WOS:000355953200025 |
| 出版者 | SPRINGER |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/276508]  |
| 专题 | 药物发现与设计中心 |
| 通讯作者 | Zhu, Weiliang |
| 作者单位 | 1.UCB Pharma, Dept Informat, Slough SL1 4EN, Berks, England; 2.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, Chem Biol Core Facil, Shanghai 200031, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, Key Lab Receptor Res, Shanghai 201203, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Yang, Zhuo,Liu, Yingtao,Chen, Zhaoqiang,et al. A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions[J]. JOURNAL OF MOLECULAR MODELING,2015,21(6). |
| APA | Yang, Zhuo.,Liu, Yingtao.,Chen, Zhaoqiang.,Xu, Zhijian.,Shi, Jiye.,...&Zhu, Weiliang.(2015).A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions.JOURNAL OF MOLECULAR MODELING,21(6). |
| MLA | Yang, Zhuo,et al."A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions".JOURNAL OF MOLECULAR MODELING 21.6(2015). |
入库方式： OAI收割
来源：上海药物研究所
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